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The Bytedeco JavaCPP library for Icy

https://github.com/bytedeco/javacpp

Fast Fourier Transform Plugin for Icy

Plugin Library used to provide autocompletion to JTextComponents, such as JTextArea or JTextField.

MetroloSPIM plugin for Icy

Tools to measure tracking performance with the ISBI Challenge on Single-Particle Tracking metrics.

I adapted and copied code from by N. Chenouard, F. De Chaumon and S. Dallongeville so that it can run in batch and without Icy.

B-spline registration adaptation for ICY based on BunwarpJ plugin from ImageJ

Big Image Tools - Read and write large 2D images with Icy

Clipper - A polygon clipping library

Minimum Spanning Tree-based clustering

Inferring alien oligonucleotides (adapters, primers, ...) from FASTQ file

creating figures that represent the positions of long repeats in a chromosome